Sequencing nucleic acids via surface enhanced Raman spectroscopy

Abstract

A Surface-Enhanced Raman Spectroscopy (SERS) device to perform accurate label-free long-read DNA sequencing. A Raman sensor has a hot spot defined by plasmonic nanostructures and excited by at least one laser. An immobilized DNA polymerase can be used to pull a DNA template strand to be sequenced through the hot spot.

What is claimed is: 
     
       1. A method of sequencing a DNA strand, comprising:
 passing the DNA strand through a nanochannel hot spot of a Raman sensor bounded by plasmonic nanostructures and excited by at least one laser; 
 identifying the nucleotides of a first section of the DNA strand present in the nanochannel at a first period in time by a Raman signature, and identifying the nucleotides of a second section of the DNA strand present in the nanochannel at a second period in time by a second Raman signature; and 
 comparing the identified nucleotides of the first section to the identified nucleotides of the second section to identify a change. 
 
     
     
       2. The method of  claim 1 , wherein passing the DNA strand comprises passing a DNA template strand. 
     
     
       3. The method of  claim 2 , wherein passing the DNA template strand comprises pulling the DNA template strand via a DNA polymerase. 
     
     
       4. The method of  claim 3 , wherein pulling the DNA template strand via the DNA polymerase includes building a complementary strand from a plurality of individual free nucleotides. 
     
     
       5. The method of  claim 1  wherein passing the DNA strand comprises pulling the DNA strand via a DNA exonuclease. 
     
     
       6. The method of  claim 1  further comprising moving the template DNA strand to the nanochannel by electrophoresis or magnetophoresis. 
     
     
       7. The method of  claim 1 , where passing the DNA strand comprises passing the DNA strand through the nanochannel hot spot of a Raman sensor bounded by two gold plasmonic nanostructures, each excited by a laser. 
     
     
       8. A method of sequencing a DNA strand, comprising:
 passing the DNA strand through a nanochannel hot spot of a Raman sensor bounded by plasmonic nanostructures and excited by at least one laser; 
 identifying a Raman signature of at least one nucleotide of a first section of the DNA strand present in the nanochannel at a first period in time, and identifying a second Raman signature of at least one nucleotide of a second section of the DNA strand present in the nanochannel at a second period; 
 comparing the Raman signature of the first section to the second Raman signature of the second section to identify a change in the Raman signature; and 
 correlating the change in the Raman signature to a single nucleotide. 
 
     
     
       9. The method of  claim 8 , wherein passing the DNA strand comprises passing a DNA template strand. 
     
     
       10. The method of  claim 9 , wherein passing the DNA template strand comprises pulling the DNA template strand via a DNA polymerase. 
     
     
       11. The method of  claim 10 , wherein pulling the DNA template strand via the DNA polymerase includes building a complementary strand from a plurality of individual free nucleotides. 
     
     
       12. The method of  claim 8  wherein passing the DNA strand comprises pulling the DNA strand via a DNA exonuclease. 
     
     
       13. The method of  claim 8  further comprising moving the template DNA strand to the nanochannel by electrophoresis or magnetophoresis. 
     
     
       14. The method of  claim 8 , where passing the DNA strand comprises passing the DNA strand through a nanochannel hot spot of a Raman sensor bounded by two gold plasmonic nanostructures, each excited by a laser. 
     
     
       15. A Surface-Enhanced Raman Spectroscopy (SERS) sensor comprising:
 a sample loading channel for receiving a DNA strand to be sequenced; 
 a secondary chamber having an immobilized DNA polymerase therein; 
 a nanochannel fluidly connecting the sample loading chamber and the secondary chamber; 
 a SERS hot spot within the nanochannel downstream of the sample loading chamber and defined by at least two plasmonic nanostructures each having a laser focused thereon, the SERS hot spot sized to receive the DNA strand therethrough; 
 a Raman detector operably connected to the SERS hot spot to measure Raman spectra from nucleotides of the DNA strand; and 
 the secondary chamber downstream of the SERS hot spot. 
 
     
     
       16. The SERS sensor of  claim 15 , wherein the sample loading chamber is for receiving a DNA template strand to be sequenced. 
     
     
       17. The SERS sensor of  claim 15 , further comprising at least one light filter operably connected to the Raman detector. 
     
     
       18. The SERS sensor of  claim 15 , comprising four plasmonic nanostructures, the four plasmonic nanostructures arranged as two pairs. 
     
     
       19. The SERS sensor of  claim 18 , wherein a first pair of plasmonic nanostructures is upstream of a second pair of plasmonic nanostructures, with each pair of plasmonic nanostructures having a laser focused thereon defining a SERS hot spot. 
     
     
       20. The SERS sensor of  claim 15  further comprising a waveguide optically connected to each of the at least two plasmonic nanostructures.